Releases · Clinical-Genomics/scout

[4.101]

Changed

Institutes are now sorted by ID on gene panels page (#5436)
Simplified visualization of previous ACMG and CCV classifications for a variant on variantS page (#5439 & #5440)
On ClinVar multistep submission form, skip fetching transcript versions for build 38 transcripts which are not MANE Select or MANE Plus Clinical (#5426)

Fixed

Malformatted table cell for analysis date on caseS page (#5438)
Remove "Add to ClinVar submission" button for pinned MEI variants as submission is not supported at the moment (#5442)
Clinical variant files could once again be read in arbitrary order on load (#5452)
Fix test_sanger_validation test to be run with a mock app instantiated (#5453)

[4.100.2]

Fixed

Keyerror 'ensembl_transcript_id' when loading transcripts from a pre-downloaded Ensembl transcripts file (#5435)

[4.100.1]

Fixed

Removed an extra x from compounds functional annotation cells (#5432)

[4.100]

Added

Button with link to cancerhotspots.org on variant page for cancer cases (#5359)
Link to ClinGen ACMG CSPEC Criteria Specification Registry from ACMG classification page (#5364)
Documentation o 8000 n how to export data from the scout database using the command line (#5373)
Filter cancer SNVs by ClinVar oncogenicity. OBS: since annotations are still sparse in ClinVar, relying solely on them could be too restrictive (#5367)
Include eventual gene-matching WTS outliers on variantS page (Overlap column) and variant page (Gene overlapping non-SNVs table) (#5371)
Minor Allele Frequency (HiFiCNV) IGV.js track for Nallo cases (#5401)
A page showing all cases submitted to the Matchmaker Exchange, accessible from the institute's sidebar (#5378)
Variants' loader progress bar (#5411)

Changed

Allow matching compounded subcategories from SV callers e.g. DUP:INV (#5360)
Adjust the link to the chanjo2 gene coverage report to reflect the type of analyses used for the samples (#5368)
Gene panels open in new tabs from case panels and display case name on the top of the page (#5369)
When uploading research variants, use rank threshold defined in case settings, if available, otherwise use the default threshold of 8 (#5370)
Display genome build version on case general report (#5381)
On pull request template, fixed instructions on how to deploy a branch to the development server (#5382)
On case general report, when a variant is classified (ACMG or CCV), tagged, commented and also dismissed, will only be displayed among the dismissed variants (#5377)
If case is re-runned/re-uploaded with the --keep-actions tag, remember also previously assigned diseases, HPO terms, phenotype groups and HPO panels (#5365)
Case load config alias and updated track label for TIDDIT coverage tracks to accommodate HiFiCNV dito (#5401)
On variants page, compounds popup table, truncate the display name of compound variants with display name that exceeds 20 characters (#5404)
Update dataTables js (#5407)
Load variants command prints more clearly which categories of variants are being loaded (#5409)
Tooltips instead of popovers (no click needed) for matching indicators on variantS page (#5419)
Call chanjo2 coverage completeness indicator via API after window loading completes (#5366)
On ClinVar multistep submission form, silence warnings coming from missing HGVS version using Entrez Eutils (#5424)

Fixed

Style of Alamut button on variant page (#5358)
Scope of overlapping functions (#5385)
Tests involving the variants controllers, which failed when not run in a specific order (#5391)
Option to return to the previous step in each of the steps of the ClinVar submission form (#5393)
chanjo2 MT report for cases in build 38 (#5397)
Fixed some variantS view tests accessing database out of app context (#5415)
Display of matching manual rank on the SV variant page (#5419)
Broken scout setup database command (#5422)
Collecting and removing ClinVar submission data for cases which have been removed (#5421)
Speed up query for gene overlapping variants (#5413)

[4.99]

Added

De novo assembly alignment file load and display (#5284)
Paraphase bam-let alignment file load and display (#5284)
Parsing and showing ClinVar somatic oncogenicity anontations, when available (#5304)
Gene overlapping variants (superset of compounds) for SVs (#5332)
Gene overlapping variants for MEIs (#5332)
Gene overlapping variants for cancer (and cancer_sv) (#5332)
Tests for the Google login functionality (#5335)
Support for login using Keycloak (#5337)
Documentation on Keycloak login system integration (#5342)
Integrity check for genes/transcripts/exons files downloaded from Ensembl (#5353)
Options for custom ID/display name for PanelApp Green updates (#5355)

Changed

Allow ACMG criteria strength modification to Very strong/Stand-alone (#5297)
Mocked the Ensembl liftover service in igv tracks tests (#5319)
Refactored the login function into smaller functions, handling respectively: user consent, LDAP login, Google login, database login and user validation (#5331)
Allow loading of mixed analysis type cases where some individuals are fully WTS and do not appear in DNA VCFs (#5327)
Documentation available in dark mode, and expanded installation instructions (#5343)

Fixed

Re-enable display of case and individual specific tracks (pre-computed coverage, UPD, zygosity) (#5300)
Disable 2-color mode in IGV.js by default, since it obscures variant proportion of reads. Can be manually enabled (#5311)
Institute settings reset (#5309)
Updated color scheme for variant assessment badges that were hard to see in light mode, notably Risk Factor (#5318)
Avoid page timeout by skipping HGVS validations in ClinVar multistep submission for non-MANE transcripts from variants in build 38 (#5302)
Sashimi view page displaying an error message when Ensembl REST API (LiftOver) is not available (#5322)
Refactored the liftover functionality to avoid using the old Ensembl REST API (#5326)
Downloading of Ensembl resources by fixing the URL to the schug server, pointing to the production instance instead of the staging one (#5348)
Missing MT genes from the IGV track (#5339)
Paraphase and de novo assembly tracks could mismatch alignment sample labels - refactor to case specific tracks (#5357)

[4.98]

Added

Documentation on how to delete variants for one or more cases
Document the option to collect green genes from any panel when updating the PanelApp green genes panel
On the institute's filters page, display also any soft filters applied to institute's variants

Fixed

Case page patch for research cases without WTS outliers

@molucorner

🌞☁️There are several new features in this early spring cleaning release.☁️🌞

Please see below. Note in particular that due to the ClinVar refactor, saved filters with clinsig_confident_always_returned enabled will be re-saved with the new options prioritised_clivar and clinvar_trusted_revstat enabled.

🙏 Extra thanks to @molucorner for the HRD display!

Added

Software version and link to the relative release on GitHub on the top left dropdown menu
Option to sort WTS outliers by p_value, Δψ, ψ value, zscore or l2fc
Display pLI score and LOEUF on rare diseases and cancer SNV pages
Preselect MANE SELECT transcripts in the multi-step ClinVar variant add to submission process
Allow updating case with WTS Fraser and Outrider research files
Load research WTS outliers using the scout load variants --outliers-research command
Chanjo2 gene coverage completeness indicator and report from variant page, summary card
Enhanced SNV and SV filtering for cancer and rare disease cases, now supporting size thresholds (≥ or < a specified base pair length)
Option to exclude ClinVar significance status in SNVs filters form
Made HRD a config parameter and display it for cancer cases.
Preset institute-level soft filters for variants (filtering based on "filters" values on variant documents). Settings editable by admins on the institute's settings page. Allows e.g. hiding tumor in_normal and germline_risk filter status variants.
Load pedigree and sex check from Somalier, provided by e.g. the Nallo pipeline
Expand the command line to remove more types of variants. Now supports: cancer, cancer_sv, fusion, mei, outlier, snv, str, and sv.
New prioritise_clinvar checkbox on rare diseases cases, SNVs page, used by clinical filter or for expanding the search to always return variants that match the selected ClinVar conditions
ClinVar CLNSIG Exclude option on cancer variantS filters

Changed

Do not show overlapping gene panels badge on variants from cases runned without gene panels
Set case as research case if it contains any type of research variants
Update igv.js to 3.2.0
IGV DNA alignment track defaults to group by tag:HP and color by methylation (useful for LRS), and show soft-clips
Update gnomAD constraint to v4.1
HG38 genes track in igv.js browser, to correctly display gene names
Refactored code for prioritizing the order of variant loading
Modified the web pages body style to adapt content to smaller screens
Refactored filters to filter variants by ClinVar significance, CLINSIG Confident and ClinVar hits at the same time
Improved tooltips for ClinVar filter in SNVs filter form
showSoftClips parameter in igv.js is set to false by default for WES and PANEL samples

Fixed

Don't save any "-1", "." or "0" frequency values for SNVs - same as for SVs
Downloading and parsing of genes from Ensembl (including MT-TP)
Don't parse SV frequencies for SNVs even if the name matches. Also accept "." as missing value for SV frequencies.
HPO search on WTS Outliers page
Stop using dynamic gene panel (HPO generated list) for clinical filter when the last gene is removed from the dynamic gene panel
Return only variants with ClinVar annotation when ClinVar hits checkbox is checked on variants search form
Legacy variant filter option clinsig_confident_always_returned on saved filters is remapped as prioritised_clivar and clinvar_trusted_revstat
Variants queries excluding ClinVar tags without prioritise_clinvar checkbox checked

What's Changed

Add software version and link to the GitHub release on the top left dropdown by @northwestwitch in #5205
Fix parse neg AF by @dnil in #5207
No overlapping panels badge if overlapping panels are 0 by @northwestwitch in #5210
Sort WTS outliers by p_value, Δψ, ψ value, zscore or l2fc by @northwestwitch in #5213
Fix parsing of entire Ensembl documents - including MT-TP gene by @northwestwitch in #5218
pLI scores on SNV and cancer SNV pages by @northwestwitch in #5209
Set case as research case if it contains any type of research variants by @northwestwitch in #5225
Fix #5230 - IGV v3.1.4 and more aln track defaults by @dnil in #5233
Fix #5227 - update gnomAD constraint to 4.1 by @dnil in #5228
Fix #5214 - parse SV freq only for SVs, accept . as missing value by @dnil in #5215
Preselect MANE SELECT transcripts in the ClinVar multistep form by @northwestwitch in #5238
Fix #5235 - fraser and outrider research update case by @dnil in #5236
Change genes 38 track in igv.js by @northwestwitch in #5240
Refactor variants loading prio by @northwestwitch in #5234
Fix #5237 - enable HPO searches on WTS outlier page by @dnil in #5243
Attempt at cases page fix for smaller screens by @northwestwitch in #5242
Load research WTS outliers using the load variants command by @northwestwitch in #5241
Complete coverage indicator chanjo2 by @dnil in #5245
Variants filter by size by @northwestwitch in #5244
Group the 3 ClinVar filters together by @northwestwitch in #5006
Fix #5250 - update IGV.js to 3.2.0 by @dnil in #5251
Ordered filters by @northwestwitch in #5257
Better ClinVar tooltips and added exclude clinsig status for SNVs filter by @northwestwitch in #4993
Make HRD a config parameter and display for cancer cases. by @molucorner in #5262
Institute-level soft filters for variants by @northwestwitch in #5254
Fix #5258 - stop clinical filter HPO when dynamic gene panel is emptied by @dnil in #5259
Fix #2177 - load somalier files by @dnil in #5260
Remove any variant type by @northwestwitch in #5219
Prioritise ClinVar checkbox by @northwestwitch in #5264
preserve saved filters by @dnil in #5268
Hide soft clips in IGV for wes and panel samples by @northwestwitch in #5271
Fix exclude ClinVar + secondary filter by @northwestwitch in #5269
Fix demo file and operator priority by @dnil in #5273
Fix #5274 - exclude clnsig also on cancer variantS page by @dnil in #5275
Version 4.97 & updated libs by @northwestwitch in #5261

Full Changelog: v4.96...v4.97

[4.96]

Added

Support case status assignment upon loading (by providing case status in the case config file)
Severity predictions on general case report for SNVs and cancer SNVs
Variant functional annotation on general case report for SNVs and cancer SNVs
Version of Scout used when the case was loaded is displayed on case page and general report

Removed

Discontinue ClinVar submissions via CSV files and support only submission via API: removed buttons for downloading ClinVar submission objects as CSV files

Changed

Display STR variant filter status on corresponding variantS page
Warning and reference to Biesecker et al when using PP1/BS4 and PP4 together in ACMG classifications
Warning to not use PP4 criterion together with PS2/PM6 in ACMG classifications with reference to the SVI Recommendation for de novo Criteria (PS2 & PM6)
Button to directly remove accepted submissions from ClinVar
Upgraded libs in uv.lock file

Fixed

Release docs to include instructions for upgrading dependencies
Truncated long HGVS descriptions on cancer SNV and SNVs pages
Avoid recurrent error by removing variant ranking settings in unranked demo case
Actually re-raise exception after load aborts and has rolled back variant insertion

This release addresses

CCV scores on case reports
Multiple fixes ACMG scores on case reports; bayesian temperature could miss modifiers
The SNV classification for can now also be accessed for SVs. It is intended primarily for small SVs. ACMG SV classification for larger SVs can be reached via link to clingen, and is intended to still be reported as manual rank.
Fixes and simplifications for PanelApp panel loading

Version 4.95

Added

CCV score / temperature on case reports
ACMG SNV classification form also accessible from SV variant page
Simplify updating of the PanelApp Green panel from all source types in the command line interactive session

Changed

Clearer link to Richards 2015 on ACMG classification section on SVs and SVs variants pages
Parse HGNC Ids directly from PanelApp when updating/downloading PanelApp panels
Skip variant genotype matching check and just return True when matching causative is found in a case with only one individual/sample
Reduced number of research MEI variants present in the demo case from 17K to 145 to speed up automatic tests

Fixed

ACMG temperature on case general report should respect term modifiers
Missing inheritance, constraint info for genes with symbols matching other genes previous aliases with some lower case letters
Loading of all PanelApp panels from command line
Saving gene inheritance models when loading/updating specific/all PanelApp panels (doesn't apply to the PanelApp Green Genes panel)
Save also complete penetrance status (in addition to incomplete) if available when loading specific/all PanelApp panels (does not apply to the PanelApp Green Genes panel)
Variants and managed variants query by coordinates, which was returning all variants in the chromosome if start position was 0
Compound loading matches also "chr"-containing compound variant names

[4.94.1]

Fixed

Temporary directory generation for MT reports and pedigree files to avoid pages crashing

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

[4.101]

Changed

Fixed

[4.100.2]

Fixed

[4.100.1]

Fixed

[4.100]

Added

Changed

Fixed

[4.99]

Added

Changed

Fixed

[4.98]

Added

Fixed

Added

Changed

Fixed

What's Changed

Contributors

[4.96]

Added

Removed

Changed

Fixed

Version 4.95

Added

Changed

Fixed

[4.94.1]

Fixed

Releases: Clinical-Genomics/scout

Variant load order fix and user interface improvements

[4.101]

Changed

Fixed

Fix parsing and loading of Ensembl transcripts

[4.100.2]

Fixed

Removed an extra x from compounds functional annotation cells

[4.100.1]

Fixed

ClinVar oncogenicity filter, WTS outliers matching, Matchmaker submissions page, and MAF track for LRS IGV

[4.100]

Added

Changed

Fixed

ClinVar oncogenicity, gene overlapping SV and MEI, Keycloak support and more IGV tracks

[4.99]

Added

Changed

Fixed

Old research cases patch, improved documentation and institute filters page

[4.98]

Added

Fixed

WTS outlier research, in_normal filter, clinvar exclude, chanjo2 coverage completeness and more

Added

Changed

Fixed

What's Changed

Contributors

Expanded annotations on report, improved case status and loading support, more ACMG warnings, fixes and updates

[4.96]

Added

Removed

Changed

Fixed

Case report CCV score, PanelApp loading improvements

Version 4.95

Added

Changed

Fixed

Fixed crashing MT report and missing pedigree images

[4.94.1]

Fixed